1 Overview

This html runs association study of the features generated by scFeatures with phenotypic outcomes such as disease conditions and output a series of plots to visualise the association study result.

2 Cell type proportions

2.1 Proportion raw

The barplot shows cell type composition of the data, split by condition.

The two boxplots show the up-regulated cell type in Responder compared to the Non-responder and the down-regulated cell type, respectively. Each dot on the boxplot represent the cell type proportion of an individual for that particular cell type.

#> Removing intercept from test coefficients
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

2.2 Proportion logit

The barplot shows cell type composition with logit transformation, split by condition.

The two boxplots show the up-regulated cell type in Responder compared to the Non-responder and the down-regulated cell type, respectively. Each dot on the boxplot represent the cell type proportion (after logit transformation) of an individual for that particular cell type.

#> Removing intercept from test coefficients
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

2.3 Pairwise ratio of proportion

The barplot shows pairwise ratio of cell type proportion (ie, proportion of cell type 1 / proportion of cell type 2), split by condition.

The two boxplots show the up-regulated ratio of proportion in Responder compared to the Non-responder and the down-regulated ratio of proportion, respectively. Each dot on the boxplot represent the proportion ratio of an individual for that particular cell type.

#> Removing intercept from test coefficients
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

3 Cell type specific gene expressions

3.1 gene mean celltype

The heatmaps show the up-regulated gene in Responder compared to the Non-responder and the down-regulated gene, respectively, for each cell type. Value represents average gene expression. The top 50 genes are shown for readability.

The enrichment plots show enrichment in biological pathways of the top 200 up-regulated or down-regulated genes in each cell type. Top 10 pathways are shown.

#> [1] "==========CD8, T Effector Memory=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Cytotoxic CD8=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Naive T Cells=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========CD8, T Effector Memory=========="
#> [1] "up regulated"

#> [1] "down regulated"

#> [1] "==========Cytotoxic CD8=========="
#> [1] "up regulated"

#> [1] "down regulated"

#> [1] "==========Naive T Cells=========="
#> [1] "up regulated"

#> [1] "down regulated"

3.2 gene proportion celltype

The heatmaps show the up-regulated gene in Responder compared to the Non-responder and the down-regulated gene, respectively, for each cell type. Value represents average proportion of expression (ie, across all cells, the percentage of cells that express a particular gene). The top 50 genes are shown for readability.

The enrichment plots show enrichment in biological pathways of the top 200 up-regulated or down-regulated genes in each cell type. Top 10 pathways are shown.

#> [1] "==========CD8, T Effector Memory=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Cytotoxic CD8=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Naive T Cells=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========CD8, T Effector Memory=========="
#> [1] "up regulated"

#> [1] "down regulated"

#> [1] "==========Cytotoxic CD8=========="
#> [1] "up regulated"

#> [1] "down regulated"

#> [1] "==========Naive T Cells=========="
#> [1] "up regulated"

#> [1] "down regulated"

3.3 gene correlation celltype

The heatmaps show the up-regulated gene in Responder compared to the Non-responder and the down-regulated gene, respectively, for each cell type. Value represents correlation in expression. The top 50 genes are shown for readability.

The enrichment plots show enrichment in biological pathways of the top 200 up-regulated or down-regulated genes in each cell type. Top 10 pathways are shown.

#> [1] "==========CD8, T Effector Memory=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Cytotoxic CD8=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Naive T Cells=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

4 Cell type specific pathway expression

4.1 pathway gsva

The heatmaps show the up-regulated pathway in Responder compared to the Non-responder and the down-regulated gene, respectively, for each cell type. Value represents pathway scores calculated using GSVA.

#> [1] "==========CD8, T Effector Memory=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Cytotoxic CD8=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Naive T Cells=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

4.2 pathway mean

The heatmaps show the up-regulated pathway in Responder compared to the Non-responder and the down-regulated gene, respectively, for each cell type. Value represents expression values of the genes in each pathway.

#> [1] "==========CD8, T Effector Memory=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Cytotoxic CD8=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Naive T Cells=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

4.3 pathway proportion

The heatmaps show the up-regulated pathway in Responder compared to the Non-responder and the down-regulated gene, respectively, for each cell type. Value represents proportion expression of genes in each pathway.

#> [1] "==========CD8, T Effector Memory=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Cytotoxic CD8=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "==========Naive T Cells=========="
#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

5 Cell type specific cell-cell communications

Heatmap shows the up-regulated cell cell interaction pair in Responder compared to the Non-responder and the down-regulated gene, respectively, for each cell type. Value represents cell cell interaction score.

#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

Heatmap and and network plot indicates the difference in the number of cell-cell interaction pairs between Responder and Non-responder. Red indicates a positivie difference (ie, greater in Responder) and blue indicates a negative difference (ie, greater in Non-responder).

6 Overall aggregated gene expressions

6.1 gene mean aggregated

The heatmaps show the up-regulated gene in Responder compared to the Non-responder and the down-regulated gene, respectively. Value represents average gene expression. The top 50 genes are shown for readability.

The enrichment plots show enrichment in biological pathways of the top 200 up-regulated or down-regulated genes in each cell type. Top 10 pathways are shown.

#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "up regulated"

#> [1] "down regulated"

6.2 gene proportion aggregated

The heatmaps show the up-regulated gene in Responder compared to the Non-responder and the down-regulated gene, respectively. Value represents average proportion of expression (ie, across all cells, the percentage of cells that express a particular gene). The top 50 genes are shown for readability.

The enrichment plots show enrichment in biological pathways of the top 200 up-regulated or down-regulated genes in each cell type. Top 10 pathways are shown.

#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

#> [1] "up regulated"

#> [1] "down regulated"

6.3 gene correlation aggregated

The heatmaps show the up-regulated gene in Responder compared to the Non-responder and the down-regulated gene, respectively. Value represents correlation in expression. The top 50 genes are shown for readability.

The enrichment plots show enrichment in biological pathways of the top 200 up-regulated or down-regulated genes in each cell type. Top 10 pathways are shown.

#> [1] "up regulated in Responder"

#> [1] "down regulated in Responder"

7 Spatial metrics

7.1 L function

The heatmaps show the up-regulated cell type pairs in Responder compared to the Non-responder and the down-regulated cell type pairs, respectively. Value represents L score. The top 50 cell type pairs are shown for readability.

#> [1] "up regulated in WT"

#> [1] "down regulated in WT"

7.2 cell type interaction

The heatmaps show the up-regulated cell type pairs in Responder compared to the Non-responder and the down-regulated cell type pairs, respectively. Value represents interaction score.

#> Warning: Zero sample variances detected, have been offset away from zero
#> [1] "up regulated in WT"

#> [1] "down regulated in WT"

7.3 Moran’s I

The heatmaps show the up-regulated genes in Responder compared to the Non-responder and the down-regulated genes, respectively. Value represents Moran’s I value.

#> [1] "up regulated in WT"

#> [1] "down regulated in WT"

7.4 nearest neighbour correlation

The heatmaps show the up-regulated genes in Responder compared to the Non-responder and the down-regulated gene, respectively. Value represents nearest neighbour correlation score.

#> [1] "up regulated in WT"

#> [1] "down regulated in WT"